Genome-wide characterization of sulphur metabolism gene families and recombination dynamics in mangrove-derived <i>Bacillus aryabhattai</i> NM1-A2 and <i>Bacillus cereus</i> NR1

This study presents a comprehensive genome-wide analysis of sulphur metabolism-related gene families in <i>Bacillus aryabhattai</i> strain NM1-A2 and <i>Bacillus cereus</i> strain NR1, isolated from marine mangrove habitats. We investigated phylogenetic relationships, conserved motifs, recombination events and physicochemical properties of sulphur metabolism genes. Phylogenetic analysis identified 4 major clades (35 genes in NM1-A2 and 34 in NR1), highlighting significant evolutionary relationships. Multiple Expectation Maximization for Motif Elicitation analysis revealed ten conserved motifs, including domains associated with cysteine/methionine metabolism and sulfurtransferases, validated by Pfam and CDD databases. Recombination analysis detected 87 and 64 putative recombination events in NM1-A2 and NR1, respectively, with significant PHI test results (<i>P</i><0.00001), suggesting distinct parental contributions. Physicochemical characterization indicated that sulphur metabolism proteins in both strains exhibit an acidic nature, instability and hydrophobicity, with minimal thermostability. Eleven gene pairs in NM1-A2 and nine in NR1 were identified under purifying selection. Recombination breakpoints were detected at site 682 in NM1-A2 and site 2397 in NR1 using Genetic Algorithm Recombination Detection. Secondary structure analysis showed disorder percentages of 0-19% in NM1-A2 and 0-16% in NR1, with alpha-helical and beta-sheet and TM helix composition variations. These findings provide new insights into the evolutionary dynamics, functional diversity and structural adaptations of sulphur metabolism genes in marine <i>Bacillus</i> strains, enhancing our understanding of their ecological roles in mangrove ecosystems.